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setup.py
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setup.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup, find_packages
requirements = [
"kipoi>=0.6.12",
#$"git+ssh://[email protected]/DerThorsten/kipoi.git@niceparse",#egg=kipoi,
"kipoi-utils>=0.1.12",
# vep
"pyvcf",
"cyvcf2",
"pybedtools",
"pysam", # required by pybedtools
"intervaltree<3",
"deepdish",
"matplotlib",
"seaborn",
"shapely",
"descartes",
# TODO - which requirements to we need?
"future",
"numpy",
"pandas",
"tqdm",
"related>=0.6.0",
"enum34",
"colorlog",
"cookiecutter",
# sometimes required
"h5py",
"urllib3>=1.21.1", #,<1.23",
]
test_requirements = [
"bumpversion",
"wheel",
"jedi",
"epc",
"pytest>=3.3.1",
"pytest-xdist", # running tests in parallel
"pytest-pep8", # see https://github.com/kipoi/kipoi/issues/91
"pytest-cov",
"coveralls",
"scikit-learn",
"cython",
# "genomelake",
"keras",
"tensorflow",
"kipoiseq"
]
setup(
name='kipoi_veff',
version='0.3.1',
description="kipoi_veff: variant effect prediction plugin for Kipoi",
author="Kipoi team",
author_email='[email protected]',
url='https://github.com/kipoi/kipoi-veff',
long_description="kipoi_veff: variant effect prediction plugin for Kipoi",
packages=find_packages(),
install_requires=requirements,
extras_require={
"develop": test_requirements,
},
# entry_points={'console_scripts': ['kipoi_veff = kipoi_veff.__main__:main']},
license="MIT license",
zip_safe=False,
keywords=["variant effect prediction", "model zoo", "deep learning",
"computational biology", "bioinformatics", "genomics"],
test_suite='tests',
include_package_data=True,
tests_require=test_requirements
)